What Is Science

Science is knowledge based on experimentation

Science cannot answer ALL the questions
Science evolves as technology evolves
Science progresses, it is continuously revised and learned
Science empowers us with knowledge, including knowledge of what we do not know
Scientific Method
 Welcome to Sections 02 and 04:
Micro-Immuno “Flavor”
• Biology changes at an extraordinary pace
• These changes create new opportunities to improve our health,
but create novel ethical issues
• We need factual knowledge to be able to understand and discuss
in a meaningful way such opportunities and ethical issues
• I will dedicate a fraction of our lecture time to introduce you to basic
concepts and language in Biology
• We need to keep updated with the scientific literature to
appreciate the excitement brought about by novel techniques
and discoveries.
• I will bring up news when they are available so that you will be able to
appreciate the value of factual knowledge and most importantly the
speed at which our knowledge increases with technical advances
 Welcome to Sections 02 and 04:
Micro-Immuno “Flavor”
• Macromolecules of life
• Cells
• Interactions between molecules, cells and organisms
• Energy flow
• Genetics
• Molecular biology
• Evolution, co-evolution
• Ecology
• Some individual infectious diseases in detail and how our
immune system deals with them
How Does Science Affect Your Life?
• Knowledge is power to solve problems
• Problems can be solved only if we make a
conscious effort at understanding the world around
us
Semmelweis and Childbed Fever (mid 1800’s):
Mortality Rates

• Observation:
• Mortality rates higher in women that gave birth in
HIS Hosiptal compared to other hospitals
• Mortalilty rates higher in Division 1
 Semmelweis and Childbed Fever:
Characteristics of Division 1
Hypotheses:
• Miasma
• Only male doctors. No midwives.
• Rougher .
• Different birthing position
• Laying on their back
• Next to autopsies laboratory
• Cadaverous particles
 Semmelweis and Childbed Fever:
Testing:
• Miasma
• Increase ventilation
• Only male doctors
• Gentler handling.
• Different birthing position
• Change position to side.
• Next to autopsies laboratory
• Hand washing with chlorine.
 Semmelweis and Childbed Fever:
Results and Conculsion:
• Only chlorine hand washing reduced rates of
childbed fever.
• Cadaverous particles caused childbed fever
The Birth of Epidemiology: J. Snow
London 1854
Germ Theory of Disease
 Life: ONE dictionary
Definition….
The property that distinguishes live things from dead
ones
Unit of Life is the Cell
• Inside a cell, life performs all the chemical reactions
necessary to avoid decay into equilibrium
• Make all their parts from simple raw materials found in the
environment
• Fuel chemical reactions by taking advantage of
environmental sources of energy
Prokaryotes and Eukaryotes
https://www.youtube.com/watch
?v=URUJD5NEXC8
Now it is time to be introduced to cells. This video
will help you visualize the cellular structures and will
give you an idea of what it would feel like inside a
cell.

Watch it again at home to help you visualize and

remember all the structures and their functions.
 Functions of Cellular Membranes
• Enclose the cytoplasm
• Control movement of ions and molecules, therefore
maintains the chemical environment inside the cell
• Organize enzymes
• Detect and allow responses to signals from the environment
• Promotes recognition and adhesion between cells and
between cells and the extracellular matrix
Cellular Membranes are Semi-Permeable
This Characteristic Is Essential For Life
 Membranes Are Made of Phospholipids.

Phospholipids are amphipatic. One end of the molecule is

hydrophobic and the other id hydrophilic
The Plasma Membrane Is Composed of a
Phospholipid By-layer
Phospholipid’s Membranes Also
Surround All Organelles
 Permeability of Phospholipid By-layers
Small, uncharged substances pass through;
large and/or charged substances do not

High permeability
Small nonpolar molecules
pass through rapidly

Small polar molecules

pass through more
slowly

For these there are

transport proteins

Low permeability
So, How Does Anything That Is Not
Permeable Go In and Out?
Proteins help!!!
 Active and Passive Transport
• Passive transport follows an ion/molecule
concentration gradient and does not require energy
input
• Active transport translocates ions/molecules against
their concentration gradient and therefore requires
energy input
Types of Transmembrane Movement
Allows for maintenance of Motion against concentration
unique intracellular gradient. Requires input of
environment energy. ATP
 Additional Functions of
Transmembrane Proteins
Cytoplasm
Cytoplasm is the watery medium where all the molecules
dissolved

Eukaryotic cell
 Prokaryotes: no nucleus
• Nucleoid region
• Well packaged. Half millimeter circle fits in a space less than
one hundredth its size. (average bacterial cell between .5
and 5 mm.
 Eukaryotic cells have a
membrane-bound nucleus
Nucleus & nucleolus
House DNA
Site of transcription
Nucleolus: make ribosomes

The cell’s hard drive

Some Cells Have a Cell Wall

Cell walls vary in composition. We will only discuss bacteria cell wall.
Two types of Bacteria Cell Wall

Peptidoglycan, both in Gram + and Gram -. Complex network of small peptides

and sugars. NOT to be confused with the plant cell wall. Cellulose. Polymer of
glucose.
Lipopolysaccharide is the outer wall specific of Gram Negative bacteria.
The Cell Wall Is Essential to Bacteria
• Protective function
• Helps bacteria attach to substrates
• Our immune system has specialized molecules that
recognize peptidoglycan and lipopolysaccharide
• Penicillin blocks the bacterial enzyme necessary for
cell wall synthesis. Causes bacterial cells to explode
Cytoplasm
Cytoplasm is the watery medium where all the molecules
dissolved

Eukaryotic cell
Cytoskeleton
• Animal cells do not have a cell wall. They use an
internal scaffolding (cytoskelton) to perform different
functions.
• A cell’s structure and movements is determined by
the cytoskeleton
• Highly organized protein fibers.
• Both prokaryotes and eukaryotes have cytoskeleton,
made of different types of proteins. Less developed
and understood in prokaryotes
Cytokeletal Fibers Are Made of
Building Blocks

COMPONENTS
Actin cortex. Polymerization of actin
protein monomers.
Microtubules. Polymerization of a and b
tubulin proteins
Intermediate filaments. Up 70 proteins
polymerize to make these filaments.
Eukaryote Cytoskeleton
 Mitochondria and Chloroplasts

Ribosomes

Flagella

Cell wall

Chromosome,
Circular
Membrane
 Mitochondria
All eukaryotic cells,
including plants

Aerobic Respiration

Number of mitochondria varies in different

cell types, there can be thousands
 Chloroplasts

Plants Photosynthesis
Prokaryotes and Eukaryotes

Ribosomes

Flagella

Cell wall

Chromosome,
Circular
Membrane
All cells have many features in common:
• A cell membrane or plasma membrane (phospho-lipid
bilayer)
• Separates cell from outside environment, facilitates
communication, maintains unique intracellular environment
• DNA chromosome(s)
• Genetic information
• Ribosomes for protein synthesis
• Actual structures where all proteins are made
• Cytoplasm in the cell.
• Watery environment where cellular structures are organized and
all chemical reactions take place
• Energy transformation pathways
• Metabolic pathways that allow cells to utilize energy from the
environment to fuel metabilsm
Macromolecules
• Carbohydrates
• Lipids
• Nucleic acids
• Proteins
 Ribosomes and Protein
Synthesis
• Proteins are synthesized by small structures called
ribosomes.
• Ribosomes are composed of proteins and RNA
• Ribosomes are composed of two subunits
Prokaryotes and Eukaryotes
Ribosomes
 Differences
Prokaryotes Eukaryotes
• No nucleus • Nucleus
• No endomembrane • Endomembrane system
system (ER, Golgi, (ER, Golgi lysosomes)
lysosomes) • Mitochondria and
• No mitochondria and chloroplasts
chloroplasts • Cytoskeleton
• Peptidoglycan cell wall
Eukaryotic Cell
 The Endomembrane System:
Involved in the Synthesis Delivery of Molecules

• Endoplasmic reticulum
• Golgi apparatus
• Exocityc vescicles
• Lysosmes
• Endosomes
Endoplasmic Reticulum (ER)
Smooth ER: Lacks ribosomes.
Involved in synthesis of lipids.

Rough ER:Has ribosomes

attached. Interconnected flattened
sacs. Functions to make more
membrane and to make proteins
that are inserted in the plasma
membrane, or shipped elsewhere.
 Pathway of Secreted and
Transmembrane Proteins

Transmembrane Secreted
Protein Synthesis and Transport
in Eukaryotes
How Do the Vescicles Know Where
to Go?
Cytoskeleton!!!!

vescicle trafficking cartoon via youtube

vescicle trafficking in vitro via youtube

Endocytosis and Exocytosis
Endocytosis: Uptake of Molecules and Cells
Lysosomes
• Lysosomes are the waste
disposal / recycling system of
the cell
• They sequester hazardous
enzymes that digest food,
destroy invaders, or dispose
of ailing mitochondria or
chloroplasts.
• Endosomes (vesicles
resulting from endocytosis,
fuse with lysosmes. In the
resulting fusion vesicle
digestion occurs
 Amoeba’s Dinner

http://www.youtube.com/watch?v
=Z_mXDvZQ6dU
Phagocytes
• Endocytosis is used by a family of immune cells
known as phagocytes that employ this mechanism to
destroy pathogens
Neutrophil Fights Bacteria

http://www.youtube.com/watch?v
=aWItglvTiLc
 Four Eons
200,000 years ago.
Homo sapiens

Macro-fossils

Eukaryotic cells,
still single cell
organisms

Life, single cells,

prokaryotic cells

68
EG Nisbet & NH Sleep, 2001. The habitat and nature of early life. Nature 409:1083-1091
Oxygen Revolution

69
EG Nisbet & NH Sleep, 2001. The habitat and nature of early life. Nature 409:1083-1091
 Mitochondria and Chloroplasts

• Note: both mitochondria and chloroplasts have

compartments surrounded by a double membrane.
• This inter-membrane space is essential for the building of a
proton gradient used to release energy for the synthesis of
ATP during aerobic respiration and photosynthesis.
 Inner Membrane Enzymes

Proton Pumps.
Aerobic Respiration in Bacteria
 Three Domains of life.
Two basic cell plans.
Prokaryote Eukaryote

Mitochondria
Nucleus

UNICELLULAR and
MULTICELLULAR

EXCLUSIVELY UNICELLULAR
Evolution of Early Anaerobic Eukaryote
Nuclear Membrane and Endomembrane System

The nucleus and endomembrane system of eukaryotes probably evolved

from infoldings of the plasma membrane of ancestral prokaryotes

Plasma membrane Cytoplasm Endoplasmic reticulum

Nucleus
Nuclear
envelope

Ancestral prokaryote Cell with nucleus and endomembrane system

 The Origin of Mitochondria and
Chloroplasts
• The endosymbiotic theory
• Larger anaerobic eukaryotes engulfed aerobic prokaryotes,
which became endosymbionts that enabled the host cell to
become aerobic.
 Reduced carbon Electron transport High ATP
Reduced carbon Fermentation Low ATP compounds + O2 yield
chain
compounds yield

Eukaryote supplies
bacterium with
reduced carbon
compounds.
bacterium supplies
eukaryote with ATP.

Photosynthesis allows
Eukaryote to produce its own organic
molecules
Rickettsia, the Ancestor of Our Mitochondria

Totally dependent on their host for reproduction

Many genomic similarities with mitochondria
Cannot manufacture building blocks of DNA
Also depend on host for synthesis of some essential constituents
Evidence supporting endosymbiotic origin

• Both mitochondria and chloroplasts are the appropriate size

• The inner membranes of mitochondria and chloroplasts have several enzymes and transport
system that resemble those found on the plasma membrane of modern prokaryotes
• Mitochondria and chloroplasts replicate by a splitting process reminiscent of binary fission
• Mitochondria and chloroplasts have a circular chromosome not associated with histones
(proteins)
• Mitochondria and chloroplasts contain rRNA, ribosomes and other equipment needed to
transcribe and translate their DNA into proteins.
Mitochondrial Genome

Less selective pressures on genes (host

provided functions) have allowed the loss
of many original genes
Also, Horizontal Gene transfer has
moved many bacterial genes to the
nuclear genome.
Genetic code shows differences

Size=16.6 kb, 13 genes in human

Eukaryotes are a bacterial and archaea merger.
Confirmed by DNA analysis
 Horizontal Gene Transfer:
Eukaryotes
• Information processing (copying DNA)-archaean
• Housekeeping (making proteins, ATP)-bacteria